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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactctttaatatccttgccaaaaaggtaactcttaatttattttgcttctataggtacatcctggtgtttgtattttatttaagcgacttcttttttgcagAATTCGTACAGGTTTTGTCTCGCTCACACCTCAAAATGCGGGTCTGGGAACGTGGTGCTG

Basic information

species Zea mays
transcript AC182617.3_FGT001
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC182617.3_FGT001 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g37960.1 (Oryza sativa), 3'ss of exon 6
gtaactctttaatatccttgccaaaaaggtaactcttaatttattttgcttctataggtacatcctggtgtttgtattttatttaagcgacttcttttttgcagAATTCGTACAGGTTTTGTCTCGCTCACACCTCAAAATGCGGGTCTGGGAACGTGGTGCTG
            ||  |||    |  |   |||  |  ||   || |  |  || |     || || |  |||| | |||| ||||   | || | || ||||||||| ||| ||||  ||||||||||||||||||||||| | |||||||| ||||||||||
----------gttactcttaattattatagaaccgt--atgccttctattcataca----tattcttgcatttg-agtttacttaaattaattttcttctgcagAATTTGTAGAGGTCCTGTCTCGCTCACACCTCAAAATGAGAGTCTGGGAGCGTGGTGCTG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|32863340|gb|CF003022.1|CF003022
EST:     TGGGCCTAAATTTGAGCATCATGAAATGTTTCCTGCTCGCACAAACACAG                         AATTCGTACAGGTTTTGTCTCGCTCACACCTCAAAATGCGGGTCTGGGAAC
genomic: TGGGCCTAAATTTGAGCATCATGAAATGTTTCCTGCTCGCACAAACACAGgtaactcttt ... ttttttgcagAATTCGTACAGGTTTTGTCTCGCTCACACCTCAAAATGCGGGTCTGGGAAC




















RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 53

GTATTGCAGGTCGACGATTTAAAACTTAGCGAAATTGGGCCTAAATTTGAGCATCATGAAATGTTTCCTGCTCGCACAAACACAGgtaactcttt ... ttttttgcagAATTCGTACAGGTTTTGTCTCGCTCACACCTCAAAATGCGGGTCTGGGAACGTGGTGCTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 87

GTATTGCAGGTCGACGATTTAAAACTTAGCGAAATTGGGCCTAAATTTGAGCATCATGAAATGTTTCCTGCTCGCACAAACACAGgtaactcttt ... ttttttgcagAATTCGTACAGGTTTTGTCTCGCTCACACCTCAAAATGCGGGTCTGGGAACGTGGTGCTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 71

GTATTGCAGGTCGACGATTTAAAACTTAGCGAAATTGGGCCTAAATTTGAGCATCATGAAATGTTTCCTGCTCGCACAAACACAGgtaactcttt ... ttttttgcagAATTCGTACAGGTTTTGTCTCGCTCACACCTCAAAATGCGGGTCTGGGAACGTGGTGCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 69

GTATTGCAGGTCGACGATTTAAAACTTAGCGAAATTGGGCCTAAATTTGAGCATCATGAAATGTTTCCTGCTCGCACAAACACAGgtaactcttt ... ttttttgcagAATTCGTACAGGTTTTGTCTCGCTCACACCTCAAAATGCGGGTCTGGGAACGTGGTGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctataggtacatcctggtgtttgtattttatttaagcgacttcttttttgcagAATTCGTACAGGTTTTGTCTCGCTCACACCTCAAAATGCGGGTCTGGGAACGTGGTGCTG
                                         cttcttttttgc  CT-rich tract
                   tgtttgtattttattt  TA-rich tract